genotypes were performed by SNPTEST (http://www.stats.ox.ac.uk/~marchini/software/gwas/snptest.html), which can handle genotype imputation uncertainty. CNV calls were generated by PennCNV (http://www. openbioinformatics.org/penncnv/) on genotyping signal intensity data. For CNV validation by multiplex ligation-dependent probe amplification (MLPA), we used the Universal Probe Library system from Roche, and all reactions were performed in triplicate with an ABI Prism 7900HT Sequence Detection System (Applied Biosystems). For CNV validation by quantitative PCR (qPCR), TaqMan probes were custom-designed using Primer Express 3.0 (Applied Biosystems). For in situ hybridization, multiple sagittally sectioned human fetal brains were obtained from the Developmental Brain and Tissue Bank at the University of Maryland. Riboprobes against CDH9 or CDH10 were used for hybridization. The SNPExpress database and software (http://people. genome.duke.edu/~dg48/SNPExpress/) were used to examine the genotype-expression relationships.
